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I'm transforming a WGS84 CRS to ETRS 89 using QGis. When I reproject the raster using via raster transformation or via GDAL Warp my pixel change from 30x30m to 26x26m which shouldn't be a problem as far as I know. When I instead save the WGS84 to ETRS89 the pixel get kind of distorted and aren't square anymore but 30x20m. The whole layer looks to be the same size either way. Can somebody explain me why this difference occurs and tell me which transformation is recommended?

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As you have experienced, Raster -> Projections -> Warp (Reproject)... is the right way to reproject with good results.

Save As ... is useful for vector data, or just saving to the same raster format under a different name or folder.

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